


The People of Atlantis VS Dr. Rodney McKay

by LdyAnne



Category: Stargate Atlantis
Genre: Alternate Universe - Canon, Angst and Humor, Drama, Episode Related, Episode: s02e16 The Long Goodbye, First Kiss, M/M
Language: English
Status: Completed
Published: 2012-05-05
Updated: 2012-05-05
Packaged: 2017-11-04 20:41:41
Rating: Teen And Up Audiences
Warnings: No Archive Warnings Apply
Chapters: 1
Words: 4,169
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/398013
Author URL: https://archiveofourown.org/users/LdyAnne/pseuds/LdyAnne
Summary: <blockquote class="userstuff">
              <p>AU Version of The Long Goodbye.  Rodney must act to defend Atlantis and John from Phoebus.</p>
            </blockquote>





	The People of Atlantis VS Dr. Rodney McKay

**Author's Note:**

> Elizabeth is mostly a plot device in this story as a means to an end. If you're an Elizabeth fan, this probably isn't a story for you.

The conference room was quiet, the mood heavy and somber. John arrived early, taking a seat at the end of the table waiting for Rodney to arrive. People arrived, trickling in in their ones and twos. There were only so many seats at the conference table and those were reserved for the people actually involved in the hearing. Everyone else squeezed in around the edges and soon the little room was full to overflowing.

The proceedings were public, but still John was surprised that so many people were showing up. Rodney was abrasive on the best of days, but he'd saved Atlantis so many times, hopefully the faces were going to be friendly, supportive ones. He wasn't surprised when Zelenka and Dr. Beckett arrived along with a few others from Rodney's division, but when Lorne showed up and nodded at him before going to stand next to Teyla, John was startled.

There was a little whispering and lots of glances at the empty seat next to John. Dr. Zelenka did try to slide into it, but when John glared at him, he went to stand next to the wall with Dr. Beckett. No one else even had the temerity to attempt to sit there. When General O'Neill and Colonel Caldwell arrived and there was still no sign of Rodney, John began to worry. It would be just like the man to make them send an escort for him.

Rodney had already proclaimed loudly and in words of many syllables why he didn't think the hearing was necessary. When John tried to explain that it was only a technicality, Rodney had responded that if it was a technicality, than he 'technically' didn't need to be there. Despite the gravity of the situation, it made John grin just to think about it.

"Did I miss something funny?" Rodney's harsh whisper jerked John back to the present. He slid into the seat with a glance around the packed room. "Because it's obvious it's not you on trial for murder."

"Oh, please, McKay," John kept his voice low so he didn't draw attention to them, "it's not a trial, it's only a hearing."

"Yes, yes, that's what you said. But if it's only a hearing then why is General O'Neill here?" Rodney's glance slid to the general where he sat with Caldwell at the head of the table. Their heads were close and their voices too low for anyone else to hear what was being said.

To be honest, that had caused John to worry a little, too. Usually generals didn't take the chance of a one-way trip to the Pegasus Galaxy on a whim. But when he'd run into Daniel Jackson walking the halls of Atlantis with a bemused smile upon his face looking like he'd died and gone to geek heaven, John suspected that might be part of what had 'persuaded' the general to make the trek.

"It's only a formality," John said in his most reassuring tone. He patted Rodney's arm, "Just tell the truth and it'll be alright."

The look Rodney threw him was indecipherable. Before he could pursue it further, the General brought the group to order.

"Now that Dr. McKay's graced us with his presence, I think it's time we began." He opened the folder in front him.

The room grew silent and all eyes turned to Rodney. Rodney's chair squeaked as he shifted, for once uncomfortable being the center of attention.

"Now then," the general began, "in the matter of The People of Atlantis VS Dr. Rodney McKay..."

John didn't hear the rest because Rodney leaned over to hiss into his ear, "See. See. See. It even sounds like a trial."

"Be quiet," John said sharply.

He was there partly to support his friend, but he was also was there to make sure Rodney wasn't unfairly accused of anything or rail-roaded. Rodney had saved John's life with his actions, along with everyone else on Atlantis and he intended to repay the debt if he could.

The general paused and threw an irritated glance in their direction before continuing, "This is not a criminal case. It's only a hearing to straighten out the details surrounding the death of Dr. Elizabeth Weir. It has generally been agreed that Dr. McKay took this severe action when it became apparent that there was no other way to keep her from killing everyone located on the Atlantis base."

"Well, to be perfectly fair," John felt he had to add, "Elizabeth was under the control of an alien soldier hell-bent on killing me at the time."

"Hey," Rodney protested, "you're supposed to be on my side."

"I am an your side, I'm just saying..."

"Gentlemen," Colonel Caldwell spoke while O'Neill just watched them with something akin to amusement lurking in his eyes. "You'll get your chance to speak, Colonel Sheppard. If we can continue?" he glowered at them both with an ironic lift of his brow.

John sat back with a small wave of his hand. "Sure, fine by me."

"Good," the general consulted the file. "Now, according to Colonel Caldwell's report..."

"Oh, come on!" Rodney objected loudly. He stood, banging his fist on the table. "You're not going to listen to him, are you? Because the man was against the whole thing from the beginning," John put a restraining hand on his arm and Rodney shook it off.

"Yes, I was and you see that I was right, too," Caldwell countered.

John knew he'd been dying to say 'I told you so,' for some time now. To be honest, John had had his doubts about the whole letting-an-alien-into-his-head thing. But when Weir and Beckett and even Rodney all assured him that it was going to be fine, he'd gone against his own instincts and agreed to play host body for the alien's consciousness for a few hours. If he were to continue being honest with himself, he'd also agreed because he really didn't want to agree with Caldwell on anything.

So, when it came right down to it, John had let an alien run rampant in his head and in his city because he wanted to prove Caldwell wrong. Gee, hadn't that turned out well?

"Gentlemen," the general's voice cut between the arguing combatants, silencing them both.

Rodney sat with an aggrieved huff. His expression clearly conveyed what kind of an idiot he considered Caldwell to be.

"Now then," the general continued, his voice laced with impatience. He frowned from one man to the other. While Caldwell maintained his military presence and didn't shrink from the general's eye, Rodney slouched in the chair, studiously not looking at anyone in the room, especially not one Colonel John Sheppard. "If we can continue...

The glare from the general might have been more effective if Daniel Jackson's voice hadn't come over the comms at that exact second.

"Jack, Jack, you have to come see this," his voice was high pitched and excited. It sounded just like Rodney's when he'd found some new power source or Ancient toy.

The general took a step back from the table and tried to turn away from all the interested eyes now focused on him, "I'd like to Daniel, but some of us have to work now. Can I call you back later? I'm kind of in the middle of something here."

"Oh, well, sure." Daniel was as oblivious to everything else as Rodney would be.

When the general turned back, his steely gaze challenged anyone in the room to make a comment. Mostly it was geniuses in the room and they were all smart enough to lower their eyes and not say a word. Although there was a lot of smirking going on.

"Now," the general ground out, "can we just get this over with before Daniel comes in here and hauls me out?"

John couldn't help the grin that broke out. It seemed they both had their geek problems.

"Colonel Caldwell, if you'll just give us the basic facts?"

John had been stuck as a prisoner in his own body while Caldwell ran the show, it was more than a little galling that he had to sit and let the other man give a report that he should have been delivering. Of course, if it had been Caldwell that the alien had hijacked, things might have turned out differently.

"Yes, sir," Caldwell stood, hands behind him at parade rest.

"At ease, Colonel," the general said, irritation in his voice. John's admiration for the general was growing in leaps and bounds.

"I... uh... yes, sir." Caldwell's posture didn't change at all as he began his report. "As I said, I was against this... idea from the beginning,"

"We know that part, Colonel," the general short circuited the argument forming on Rodney's lips before he could even say a word.

He made a 'let's move on' gesture as he said, "Yadda, yadda, yadda, they didn't listen to you and Colonel Sheppard and Dr. Weir were both taken over by alien consciousnesses. We find out that the aliens were lying to you the entire time, no surprise there, that instead of being husband and wife they were in fact mortal enemies intent on killing each other. Does that about sum up the situation?"

Caldwell looked like he was about to hack up a hair ball, but he just answered, "I... yes, sir."

John couldn't believe just how much he was enjoying himself.

"And then?" the general prompted expectantly.

"Colonel Sheppard took out the city's power supply."

"Excuse me, that would be 'the alien that hijacked Colonel Sheppard's body' took out the city's power supply," John felt it necessary to interject. He had enough black marks in his record without something like this to add to it.

"Of course, colonel, that's understood," the general said dryly, "don't get your boxers in a wad."

John heard Rodney's quiet snicker next to him.

"At least I didn't kill Elizabeth," he hissed in a whisper that only Rodney could hear.

"Hey!"

"So, the alien took out the power supply, I'm assuming Dr. McKay got it back up and running again?"

"That would be correct," Dr. McKay answered for himself. "That would be when the 'alien in Elizabeth's body'," he made little air quotes with a sideways glance to Sheppard, "found a computer terminal in the science lab and took over the city."

_Rodney had been on his way back to the control room when he'd spotted an Elizabeth-sized shape running in front of him. He knew there was nothing he could do, but he followed her anyway. When she ducked into the science lab, he'd slipped in after her, hiding in a shadowed corner behind some machinery. He tucked himself in and prepared to wait._

_He had been horrified when she'd threatened to release the halon gas into the residential quarters, but he could see that she would do it. If John wasn't killed, she'd kill three quarters of the expedition members, then she'd still go after John and kill him._

_From where he was hiding, the monitor displaying John and Teyla was visible. Teyla looked miserable as Elizabeth demanded that she kill John. Teyla wasn't going to kill John, it just wasn't in her. He could also see Elizabeth..., no Phoebus. It might look like Elizabeth, but the hatred shining in her eyes was all the alien bent on finishing her war no matter the cost in innocent lives._

_She watched the screen with narrowed eyes, her finger hovering over the button that would activate the fire suppression systems, her lips curved in a smile of anticipation._

_Those lips that had kissed John._

_Rodney could see it again, her lips on his, her body pressed against him._

_He pulled out John's gun where he'd tucked into the small of his back after being revived in the lab. John had given it to him and he intended to be the one to give it back. But now he might be able to use it to save John's life._

_"Phoebus," he called as he stepped out of the shadows._

_She jerked in surprise, "Why Dr. McKay, Dr. Weir is surprised to see you here. Shouldn't you be up in the control room trying to save the city from me?" She sneered at him, her lips curled down in disdain._

_Those lips pressed against John's..._

_He didn't bother answering because that's where he should be, in the control room, fighting her from there. But he wasn't. He was here._

_"Just step away from the computer and let me release the city's systems," he instructed. He tried to keep his hand steady on the gun the way John taught him._

_"Oh, please, like I'm really going to do that. You're not going to shoot me and risk hurting your precious Dr. Weir," she pursed her lips, waiting for him to make the next move._

_"You're threatening my city and my friends, you'd be surprised what I could do," he tried to keep the tremor out of his voice, he really did, but it was there nevertheless and she knew he wasn't going to do it. He couldn't shoot Elizabeth._

_Then she smiled in satisfaction and she ran a tongue over her lips and all he could see was Elizabeth kissing John..._

_He'd been surprised how angry it made him. It was supposed to be him kissing John and he hadn't even known that until he was presented with the specter of Elizabeth and John pressed together tightly..._

_He didn't remember pulling the trigger but the sound of the shot pulled him back to reality. Elizabeth was falling then, convulsing as the alien lost its hold on the host body. He rushed to her side, dropping to his knees and, dear god, there wasn't a pulse..._

"So, you shot Dr. Weir when you saw that she was going to release the halon gas?" the general asked quietly.

There was no sound in the room, not even breathing as everyone waited for Rodney's reply.

"Well of course that's when I shot the 'alien in Dr. Weir's body'," Rodney snapped in exasperation.

What did they want him to say, that he shot her because she'd kissed John?

"That's when he called me with the medical emergency," Beckett picked up the story.

Rodney leaned back, thankful that someone else was taking over. He still felt like he was being watched. He looked over at John to find the colonel studying him intently.

"What?" he mouthed, not really anxious to draw the attention back to himself any time soon.

John just shrugged and settled back.

It didn't take long to finish at the point. Carson had shown up in the science lab, he had been able to revive Elizabeth. She was in the infirmary still recovering from the gun shot wound, following the hearing from there.

"Does that cover everything, Dr. Weir?" the general asked as the doctor finished his part of the story.

"I believe so, Jack," her disembodied voice was amplified so they could all hear it, whether they wore comms or not. "Rodney?"

He jerked, "Yes, Elizabeth?"

"I just want to thank you for... doing what you did. I was terrified that Phoebus was going to release that gas."

"I uh... yes, of course, you can depend on me to kill you whenever necessary." He didn't know what else to say, but it seemed to break the tension in the room. There was scattered laughter throughout the room.

"Well," Rodney announced, "If we're quite done here, I've got work to do before the next crisis. Just... call me if you need anyone killed."

With that he marched out stiffly out of the room not looking back.

John stared at his retreating back, bemused. There was something going on with McKay and as soon as the damned meeting was over he intended to find out what that was.

~~~~~

When the chime sounded announcing someone was at his door, Rodney ignored it. He knew who was there and he really wasn't interested in talking.

There was silence, and for a moment he actually imagined that John might have gone away. That hope was dashed when the chime sounded again. Obstinately Rodney sat at his computer refusing to acknowledge it.

John's patience didn't last a third time. He pounded on the door, "Rodney, open the damn door."

Rodney continued working, confident that John would soon grow bored and go away. Except John didn't ever go with Rodney's plans. He should have been surprised when the door slid open despite his repeated mental commands that it not do so, but he wasn't.

John stood in the now-open door, leaning casually against the frame. "Why didn't you open the door?"

"Because I didn't want to be disturbed," Rodney answered tightly, refusing to look up. "Obviously you're too dense to get that fact. Now go away."

"Why in the hell are you mad at me?" John sounded hurt and bewildered and it caught Rodney's attention.

He made the mistake of looking up and found himself trapped, staring into John's eyes. "I'm not mad at you," he snapped, forcing himself to look away, at the computer, at the floor, anywhere but into John's eyes. "Can't you see I'm busy? We wasted all afternoon with this stupid hearing and now I've got work to do."

Instead of leaving, John sauntered further into the room. He stood behind Rodney's shoulder, leaning in to peer down at the computer, "Funny you don't look all that busy. Why didn't you go to your lab if you've got so much work to do?"

Because he knew that was the first place John would look for him, but he couldn't very well tell John that. He'd hoped for a little time to regroup, to put himself together before he had to face John Sheppard again, but obviously that wasn't going to happen. He was going to have to tough it out. He could do it. He could.

"Because I knew people would be looking for me there, to congratulate me that I got away with killing Elizabeth and I... just couldn't deal with it. Okay? Happy?" He hoped John would just take the dismissal for what it was and leave.

But no, John didn't take hints. He sat on the edge of Rodney's desk, leg hooked over the edge, swinging it oh-so-casually. "So, why did you do it?" he asked conversationally.

"Do it?" Rodney's brain actually blanked. For the life of him, he couldn't figure out what John was asking.

"You know. Shoot Elizabeth. Really? Why'd you do it?" John leaned in close, eyes intent and curious. Rodney breathed in his scent, it was spicy and dangerous and utterly forbidden.

With a snort of disgust, Rodney pushed himself away from the desk. "You didn't really pass the Mensa test did you?" Briskly he walked to the other side of the room to a table strewn with notes. He rifled through them pretending he was looking for something. He hoped John didn't notice the way his hands were shaking.

"You cheated somehow, didn't you? Because, seriously that's the stupidest question I've ever heard. You sat there next to me, you heard everything, and you still want to know why I shot Elizabeth?" Rodney knew the pitch of his voice had reached the heavens, but it was beyond his control.

Rodney felt like he was being stalked. John just wouldn't take the hint and leave him alone. He followed Rodney across the room, standing behind him, leaning in against his shoulder to see the papers Rodney was holding in his hand. He was standing so close that Rodney could feel the heat of his body warming his back. Trapped between John and the table, all he'd have to do was turn and they'd be close enough that he could press his lips against John's...

He knew it was ungainly and awkward, but Rodney sidled sideways and escaped back to the other side of his room, putting the desk between himself and John. He was almost disappointed when John didn't follow him again. John just stood, hands in his pockets, rocking back on his heels, smirking.

"You remember when the city was taken by the Genii, back during the storm?" John asked it so casually, as if it had been just another day in the city.

"Like I'm ever likely to forget that," he answered roughly. Without even knowing he did it, Rodney pulled in the arm injured when the Genii tortured him for information, rubbing it absently.

"What's your point?" He needed John to leave now. It was all too much.

Maybe John could see he'd pushed too far, his easy manner disappeared. He crossed the room in two long steps and pushed the chair around for Rodney to drop into.

"Elizabeth told me what you said about not being able to lie worth a damn," John's voice was warm and concerned and amused. "You were right."

"What?" Rodney forget his anxiety over Koyla and his arm in his indignation. "What are you saying? That I lied today? That I didn't shoot Elizabeth to save Atlantis?" He started to rise, but John put a hand on his shoulder, forcing him to stay seated.

"Now hold on, I didn't say that." John said.

The fingers on Rodney's shoulder were rubbing in little circles, completely distracting him from John's words.

"I'm sure that's part of why you did... what you did."

"Part?" John paused and Rodney couldn't help it. He had to look up, meet John's eyes, see if he could tell what he was thinking. It was a mistake because John's eyes were deep and he felt like he was falling, falling into John...

"I know how you felt, because you know when you kissed Beckett that time? I really wanted to shoot him," John confessed quietly, his gaze intent.

"Now wait a minute," Rodney began indignantly, "That was so not my fault, Cadman..." he trailed off as the ramifications of what John had said percolated through his brain. "You... wanted to shoot Carson?"

John had perched a hip on the desk again. He leaned in closer and the hand on his shoulder had migrated to Rodney's neck, fingertips lightly caressing. His voice was low and Rodney hung on every word. "Yeah, I mean he got to kiss you first."

John brushed his thumb across Rodney's lips, it dragged with a delicious friction. "That was something I'd been wanting to do for a while now." The fingers moved to cup his cheek and Rodney leaned into it.

His heart was beating so loudly Rodney could barely think over the noise. He licked suddenly dry lips, "You... wanted... to kiss... me?"

"If I could ever get you to shut up long enough that I'd have an opening," he was smiling that John smile that said Rodney was an idiot but it was alright because really John liked idiots.

John's other hand had moved yet again to cup the back of his neck, his fingers moving into the short hair at his nape, curling into it, skimming the skin..

Rodney's ability to think was being seriously compromised, but he made a last ditch effort just to make sure he was clear on what John was saying, "And you think I shot Elizabeth because she kissed you?"

John didn't answer, he just leaned in the rest of the way to brush his lips across Rodney's. Rodney froze not knowing what to do for a long second. Sure he was a genius, he knew quantum physics and he saved Atlantis at least twice a week, but John Sheppard was kissing him and he was suddenly a quivering mass of jello.

It didn't seem to deter John however. He just slid his lips to the side and attacked Rodney's ear with little dropped kisses and a lick that went straight south.

"You just gonna sit there all day, McKay and let me do all the work?" his voice in Rodney's ear was a husky whisper that sent fire shooting through Rodney's body.

Rodney's brain engaged and he stood, nearly knocking heads with John.

"Sorry, sorry," he whispered as he captured John's face with a hand and turned it so he could attack John's mouth. John must have approved that plan because his mouth slid open for Rodney's tongue and it was so much better than he had ever imagined, hot and wet and eager. John took all of his kisses and returned them with a hungry need of his own.

"So, McKay," John panted into his mouth when he pulled away to breathe, "no more shooting Elizabeth, right?"

Rodney could barely think of anything besides 'don't stop kissing,' and 'too many clothes,' but he managed to gasp out, "As long as she never kisses you again. If she does, all bets are off."

Then he had John's shirt out of his pants and his hands found warm, yielding flesh and he really wasn't interested in talking about Elizabeth Weir anymore.

**Author's Note:**

> Thanks to my beta chocolatephysicist. My story is better for her comments and suggestions. Any errors remaining are my own.


End file.
